def getProgramLauncherInstance( self ):
if self._prgLauncher == None:
self._prgLauncher = MapProgramLauncher()
self._prgLauncher.setInputFile( GENERIC_IN_FILE )
self._prgLauncher.setOutputFile( "%s.fa_aln" % ( GENERIC_IN_FILE ) )
self._prgLauncher.setClean()
self._prgLauncher.setVerbosityLevel( 1 )
self._prgLauncher.setListFilesToKeep()
self._prgLauncher.setListFilesToRemove()
return self._prgLauncher
class MapClusterLauncher( AbstractClusterLauncher ):
"""
Launch Map on several files in parallel on a cluster.
"""
def __init__( self ):
"""
Constructor.
"""
AbstractClusterLauncher.__init__( self )
AbstractClusterLauncher.setAcronym( self, "Map" )
self._cmdLineSpecificOptions = "s:m:O:e:"
self._exeWrapper = "MapProgramLauncher.py"
self._prgLauncher = None
self._prgLauncher = self.getProgramLauncherInstance()
def getSpecificHelpAsString( self ):
"""
Return the specific help as a string.
"""
string = ""
string += "\nspecific options:"
string += "\n -s: size above which a gap is not penalized anymore (default='%i')" % ( self.getGapSize() )
string += "\n -m: penalty for a mismatch (default='%i')" % ( self.getMismatchPenalty() )
string += "\n -O: penalty for a gap openning (default='%i')" % ( self.getGapOpenPenalty() )
string += "\n -e: penalty for a gap extension (default='%i')" % ( self.getGapExtendPenalty() )
return string
def getGapSize( self ):
return self._prgLauncher.getGapSize()
def getMismatchPenalty( self ):
return self._prgLauncher.getMismatchPenalty()
def getGapOpenPenalty( self ):
return self._prgLauncher.getGapOpenPenalty()
def getGapExtendPenalty( self ):
return self._prgLauncher.getGapExtendPenalty()
def getProgramLauncherInstance( self ):
if self._prgLauncher == None:
self._prgLauncher = MapProgramLauncher()
self._prgLauncher.setInputFile( GENERIC_IN_FILE )
self._prgLauncher.setOutputFile( "%s.fa_aln" % ( GENERIC_IN_FILE ) )
self._prgLauncher.setClean()
self._prgLauncher.setVerbosityLevel( 1 )
self._prgLauncher.setListFilesToKeep()
self._prgLauncher.setListFilesToRemove()
return self._prgLauncher
